Welcome to RootReader3D

(return to plantmineralnutrition.net)

This site provides an introductory guide to setup, install and run RootReader3D.

RootReader3D is a Java-based1 image analysis tool to non-destructively measure 3D root system architecture (RSA) characteristics from plants grown in hydroponics or other artificial media. The analysis is generally applicable to a wide range of plant species. This software has been used to measure root lengths (e.g., Famoso et al., 2010; Clark et al., 2011; Famoso et al., 2011; Milner et al., 2012) and contains novel features and algorithms that enable both whole root system or specific root type characteristics to be quantified.

RootReader3D utilizes a silhouette-based back-projection algorithm (Mulayim et al., 2003; Zhu et al., 2006) to construct 3D models from preprocessed binary images of root systems. It adopts a template-matching technique (Kálmán and Attila 1999), followed by a valence-driven spatial median filter (Wang and Cheng, 2008) to generate unit-width skeleton representations of the root models. From the 3D models, the following 12 global root traits are measured:

Name Units Description
Centroid cm Vertical position of the center of mass of the whole root system
Convex Hull cm3 Volume formed by the convex areas (smallest convex set of voxels that contain all root voxels in a given slice) calculated for each horizontal slice through the whole root system
Max Depth cm Maximum vertical depth of whole root system
Max Width cm Maximum horizontal width of whole root system
Maximum Roots # Number of roots at the 84th percentile of a sorted list of root counts from all horizontal cross-sectional slices through the whole root system
Median Roots # Median number of roots from root counts taken from all horizontal cross-sectional slices through the whole root system
Min Width cm Minimum horizontal width of whole root system
Tip Count # Number of root tips in the whole root system based on root voxels in the skeleton that have only one 26-connected neighbor root voxel
TSL cm Total root system length based on the polyline estimation technique on root voxels in the root skeleton
TRSV cm3 Total root system volume
TRSSA cm2 Total root system surface area based on root voxel counts that are 6-connected to a background voxel
Volume Distribution cm3/cm3 Ratio of the volume of roots contained above the one-third root system depth to the volume of roots contained below the one-third root system depth

Based on these 12 trait measurements, the following 7 additional traits are calculated:

Name Units Description
Bushiness #/# Ratio of maximum number of roots to median number of roots; considered a measure of root branching complexity (Iyer-Pascuzzi et al., 2010)
Min/Max Width cm/cm Ratio of minimum to maximum horizontal root width
Max Width/Max Depth cm/cm Ratio of maximum root width to maximum root depth
Solidity cm3/cm3 Ratio of the total root volume to the volume of the convex hull
SRL cm/cm3 Specific root length taken as the ratio of the total root length to total root volume
TRSSA/TRSV cm2/cm3 Ratio of total root system surface area to total root volume
TRSL/TRSSA cm/cm2 Ratio of total root length to total root system surface area

  1. Copyright © 1995, 2017, Oracle.